Identification, Classification, and Expression Analysis of GRAS Gene Family in Malus domestica.

Sheng Fan,Mingyu Han,Dong Zhang,Cai Gao,Haiqin Wu,Yawen Shen,Ming Zhao,Youmei Li

doi:10.3389/fphys.2017.00253

Sheng Fan, Mingyu Han + Show 6 more

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https://doi.org/10.3389/fphys.2017.00253

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Abstract

GRAS genes encode plant-specific transcription factors that play important roles in plant growth and development. However, little is known about the GRAS gene family in apple. In this study, 127 GRAS genes were identified in the apple (Malus domestica Borkh.) genome and named MdGRAS1 to MdGRAS127 according to their chromosomal locations. The chemical characteristics, gene structures and evolutionary relationships of the MdGRAS genes were investigated. The 127 MdGRAS genes could be grouped into eight subfamilies based on their structural features and phylogenetic relationships. Further analysis of gene structures, segmental and tandem duplication, gene phylogeny and tissue-specific expression with ArrayExpress database indicated their diversification in quantity, structure and function. We further examined the expression pattern of MdGRAS genes during apple flower induction with transcriptome sequencing. Eight higher MdGRAS (MdGRAS6, 26, 28, 44, 53, 64, 107, and 122) genes were surfaced. Further quantitative reverse transcription PCR indicated that the candidate eight genes showed distinct expression patterns among different tissues (leaves, stems, flowers, buds, and fruits). The transcription levels of eight genes were also investigated with various flowering related treatments (GA3, 6-BA, and sucrose) and different flowering varieties (Yanfu No. 6 and Nagafu No. 2). They all were affected by flowering-related circumstance and showed different expression level. Changes in response to these hormone or sugar related treatments indicated their potential involvement during apple flower induction. Taken together, our results provide rich resources for studying GRAS genes and their potential clues in genetic improvement of apple flowering, which enriches biological theories of GRAS genes in apple and their involvement in flower induction of fruit trees.

Highlights

IntroductionGRAS genes encode a family of plant-specific transcription factors
Transcription factors function as trans-acting factors, combining with specific cis- elements in eukaryotic gene promoter regions to regulate plant growth and development.GRAS genes encode a family of plant-specific transcription factors
To identify members of the MdGRAS gene family, both Hidden Markov Model (HMM) profiles and BLASTP were used with the default parameters

Summary

Introduction

GRAS genes encode a family of plant-specific transcription factors. Proteins in the GRAS family consist of 400–700 amino acids with a conserved GRAS carboxyl. Many GRAS genes have been identified in a variety of plant species, including Prunus mume, Populus, grape, tomato, Chinese cabbage, and castor bean (Tian et al, 2004; Song et al, 2014; Huang et al, 2015; Lu et al, 2015; Grimplet et al, 2016; Xu W. et al, 2016).The GRAS family, which has 33 members in Arabidopsis thaliana and 57 members in rice (Oryza sativa), can be divided into eight subfamilies: SCL3, SHR, PAT1, LISCL, DELLA, SCR, LS, and HAM (Hirsch et al, 2009)

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